Technical Abstract: Brown midrib (bmr) mutants are being investigated for their ability to increase the conversion efficiency of sorghum biomass for lignocellulosic bioenergy. Brown midrib 6 and 12 (bmr6 and 12) are impaired the last two steps of monolignol biosynthesis resulting in reduced lignin content and altered lignin composition. Bmr6 and Bmr12 encode a cinnamyl alcohol dehydrogenase (CAD) and a caffeic acid-O-methyltransferase (COMT), respectively. To comprehensively characterize the effects of bmr6 and bmr12 have on sorghum gene expression, the Illumina platform was used to sequence nearly 200 million reads representing reverse-transcribed mRNAs from bmr and wild-type stalks. Expression profiles were generated from wild-type and near-isogenic lines containing bmr6, bmr12 or both bmr mutants in three different sorghum varieties. A database of SNPs in expressed transcripts between the three sorghum varieties profiled Atlas, R Tx430 and Wheatland compared to JGI sequenced reference genome R Tx623 was generated. Differential expressed genes were identified in bmr mutants relative to wild-type, which may connect specific gene products functions in cell wall formation, lignification or bioenergy availability. Roughly triple the number of genes were differentially expressed in bmr6 stalks relative to wild-type as compared to bmr12 relative to wild-type. Together these data demonstrate that bmr6 and bmr12 each had distinct impacts upon gene expression, which may have specific plant physiological implications.